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<h1 class="epydoc">Source Code for <a href="trunk.BIP.Bayes.PlotMeld-module.html">Module trunk.BIP.Bayes.PlotMeld</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno">  1</tt>  <tt class="py-line"><tt class="py-comment"># To change this template, choose Tools | Templates</tt> </tt>
<a name="L2"></a><tt class="py-lineno">  2</tt>  <tt class="py-line"><tt class="py-comment"># and open the template in the editor.</tt> </tt>
<a name="L3"></a><tt class="py-lineno">  3</tt>  <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L4"></a><tt class="py-lineno">  4</tt>  <tt class="py-line"><tt class="py-docstring">Module with specialized plotting functions for the Melding results</tt> </tt>
<a name="L5"></a><tt class="py-lineno">  5</tt>  <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L6"></a><tt class="py-lineno">  6</tt>  <tt class="py-line"> </tt>
<a name="L7"></a><tt class="py-lineno">  7</tt>  <tt class="py-line"><tt class="py-name">__author__</tt><tt class="py-op">=</tt><tt class="py-string">"fccoelho"</tt> </tt>
<a name="L8"></a><tt class="py-lineno">  8</tt>  <tt class="py-line"><tt class="py-name">__date__</tt> <tt class="py-op">=</tt><tt class="py-string">"$06/01/2010 11:24:20$"</tt> </tt>
<a name="L9"></a><tt class="py-lineno">  9</tt>  <tt class="py-line"><tt class="py-name">__docformat__</tt> <tt class="py-op">=</tt> <tt class="py-string">"restructuredtext en"</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt>  <tt class="py-line"> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">itertools</tt> <tt class="py-keyword">import</tt> <tt class="py-name">cycle</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">scipy</tt> <tt class="py-keyword">import</tt> <tt class="py-name">stats</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">glob</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">datetime</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">numpy</tt> <tt class="py-keyword">import</tt> <tt class="py-op">*</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">matplotlib</tt><tt class="py-op">.</tt><tt class="py-name">pyplot</tt> <tt class="py-keyword">as</tt> <tt class="py-name">P</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">matplotlib</tt><tt class="py-op">.</tt><tt class="py-name">dates</tt> <tt class="py-keyword">import</tt> <tt class="py-name">date2num</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">scipy</tt><tt class="py-op">.</tt><tt class="py-name">stats</tt> <tt class="py-keyword">import</tt> <tt class="py-name">gaussian_kde</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">pdb</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt>  <tt class="py-line"> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt>  <tt class="py-line"> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt>  <tt class="py-line"> </tt>
<a name="plot_series"></a><div id="plot_series-def"><a name="L23"></a><tt class="py-lineno"> 23</tt> <a class="py-toggle" href="#" id="plot_series-toggle" onclick="return toggle('plot_series');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.PlotMeld-module.html#plot_series">plot_series</a><tt class="py-op">(</tt><tt class="py-param">tim</tt><tt class="py-op">,</tt><tt class="py-param">obs</tt><tt class="py-op">,</tt> <tt class="py-param">series</tt><tt class="py-op">,</tt> <tt class="py-param">names</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-param">title</tt><tt class="py-op">=</tt><tt class="py-string">'series'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="plot_series-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="plot_series-expanded"><a name="L24"></a><tt class="py-lineno"> 24</tt>  <tt class="py-line">    <tt class="py-name">c</tt> <tt class="py-op">=</tt> <tt class="py-name">cycle</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">'b'</tt><tt class="py-op">,</tt><tt class="py-string">'g'</tt><tt class="py-op">,</tt><tt class="py-string">'r'</tt><tt class="py-op">,</tt><tt class="py-string">'c'</tt><tt class="py-op">,</tt><tt class="py-string">'m'</tt><tt class="py-op">,</tt><tt class="py-string">'y'</tt><tt class="py-op">,</tt><tt class="py-string">'k'</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt>  <tt class="py-line">    <tt class="py-name">ser2</tt><tt class="py-op">=</tt><tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">series</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">:</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt>  <tt class="py-line">        <tt class="py-name">ser2</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">concatenate</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">s</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">s</tt> <tt class="py-keyword">in</tt> <tt class="py-name">series</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">names</tt><tt class="py-op">:</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt>  <tt class="py-line">        <tt class="py-name">names</tt> <tt class="py-op">=</tt> <tt class="py-name">series</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt><tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">names</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt>  <tt class="py-line">        <tt class="py-comment">#print n</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt>  <tt class="py-line">        <tt class="py-comment">#P.subplot(l,1,i)</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt>  <tt class="py-line">        <tt class="py-name">co</tt> <tt class="py-op">=</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">next</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt>  <tt class="py-line">        <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">plot</tt><tt class="py-op">(</tt><tt class="py-name">tim</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">scoreatpercentile</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">,</tt><tt class="py-number">5</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">t</tt> <tt class="py-keyword">in</tt> <tt class="py-name">ser2</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">T</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">co</tt><tt class="py-op">+</tt><tt class="py-string">'-.'</tt><tt class="py-op">)</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt>  <tt class="py-line">        <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">plot</tt><tt class="py-op">(</tt><tt class="py-name">tim</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">scoreatpercentile</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">,</tt><tt class="py-number">95</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">t</tt> <tt class="py-keyword">in</tt> <tt class="py-name">ser2</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">T</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">co</tt><tt class="py-op">+</tt><tt class="py-string">'-.'</tt><tt class="py-op">)</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt>  <tt class="py-line">        <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">plot</tt><tt class="py-op">(</tt><tt class="py-name">tim</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">scoreatpercentile</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">,</tt><tt class="py-number">50</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">t</tt> <tt class="py-keyword">in</tt> <tt class="py-name">ser2</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">T</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">co</tt><tt class="py-op">+</tt><tt class="py-string">'-'</tt><tt class="py-op">,</tt><tt class="py-name">lw</tt><tt class="py-op">=</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-name">label</tt><tt class="py-op">=</tt><tt class="py-name">n</tt><tt class="py-op">)</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt>  <tt class="py-line">        <tt class="py-comment">#P.plot(tim,y[:,list(series.dtype.names).index(n)],'*',label=n+' obs.')</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">obs</tt><tt class="py-op">:</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt>  <tt class="py-line">            <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">plot</tt><tt class="py-op">(</tt><tt class="py-name">tim</tt><tt class="py-op">,</tt><tt class="py-name">obs</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-string">'*'</tt><tt class="py-op">,</tt><tt class="py-name">label</tt><tt class="py-op">=</tt><tt class="py-name">n</tt><tt class="py-op">+</tt><tt class="py-string">' obs.'</tt><tt class="py-op">)</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt>  <tt class="py-line">    <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">savefig</tt><tt class="py-op">(</tt><tt class="py-name">title</tt><tt class="py-op">+</tt><tt class="py-string">'.png'</tt><tt class="py-op">)</tt> </tt>
</div><a name="L41"></a><tt class="py-lineno"> 41</tt>  <tt class="py-line"> </tt>
<a name="plot_pred"></a><div id="plot_pred-def"><a name="L42"></a><tt class="py-lineno"> 42</tt> <a class="py-toggle" href="#" id="plot_pred-toggle" onclick="return toggle('plot_pred');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.PlotMeld-module.html#plot_pred">plot_pred</a><tt class="py-op">(</tt><tt class="py-param">tim</tt><tt class="py-op">,</tt><tt class="py-param">series</tt><tt class="py-op">,</tt><tt class="py-param">y</tt><tt class="py-op">,</tt> <tt class="py-param">fig</tt><tt class="py-op">,</tt><tt class="py-param">names</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-param">title</tt><tt class="py-op">=</tt><tt class="py-string">'series'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="plot_pred-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="plot_pred-expanded"><a name="L43"></a><tt class="py-lineno"> 43</tt>  <tt class="py-line">    <tt class="py-name">c</tt> <tt class="py-op">=</tt> <tt class="py-name">cycle</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">'b'</tt><tt class="py-op">,</tt><tt class="py-string">'g'</tt><tt class="py-op">,</tt><tt class="py-string">'r'</tt><tt class="py-op">,</tt><tt class="py-string">'c'</tt><tt class="py-op">,</tt><tt class="py-string">'m'</tt><tt class="py-op">,</tt><tt class="py-string">'y'</tt><tt class="py-op">,</tt><tt class="py-string">'k'</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">names</tt><tt class="py-op">:</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt>  <tt class="py-line">        <tt class="py-name">names</tt> <tt class="py-op">=</tt> <tt class="py-name">series</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt>  <tt class="py-line">    <tt class="py-name">l</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">names</tt><tt class="py-op">)</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt>  <tt class="py-line">    <tt class="py-name">ax</tt> <tt class="py-op">=</tt> <tt class="py-name">fig</tt><tt class="py-op">.</tt><tt class="py-name">add_subplot</tt><tt class="py-op">(</tt><tt class="py-number">111</tt><tt class="py-op">)</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt><tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">names</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt>  <tt class="py-line">        <tt class="py-name">co</tt> <tt class="py-op">=</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">next</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">b</tt> <tt class="py-keyword">in</tt> <tt class="py-op">[</tt><tt class="py-number">2.5</tt><tt class="py-op">,</tt><tt class="py-number">25</tt><tt class="py-op">,</tt><tt class="py-number">50</tt><tt class="py-op">,</tt><tt class="py-number">75</tt><tt class="py-op">,</tt><tt class="py-number">97.5</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">b</tt> <tt class="py-op">==</tt> <tt class="py-number">50</tt><tt class="py-op">:</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt>  <tt class="py-line">                <tt class="py-name">st</tt> <tt class="py-op">=</tt> <tt class="py-string">'k-'</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt>  <tt class="py-line">            <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt>  <tt class="py-line">                <tt class="py-name">st</tt> <tt class="py-op">=</tt> <tt class="py-string">'%s:'</tt><tt class="py-op">%</tt><tt class="py-name">co</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt>  <tt class="py-line">            <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt>  <tt class="py-line">                <tt class="py-name">lower</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">scoreatpercentile</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">+</tt><tt class="py-name">b</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">t</tt> <tt class="py-keyword">in</tt> <tt class="py-name">series</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">T</tt><tt class="py-op">]</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt>  <tt class="py-line">                <tt class="py-name">upper</tt> <tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">scoreatpercentile</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">,</tt><tt class="py-number">100</tt><tt class="py-op">-</tt><tt class="py-name">b</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">t</tt> <tt class="py-keyword">in</tt> <tt class="py-name">series</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">T</tt><tt class="py-op">]</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt>  <tt class="py-line">                <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">plot</tt><tt class="py-op">(</tt><tt class="py-name">tim</tt><tt class="py-op">,</tt><tt class="py-name">lower</tt><tt class="py-op">,</tt><tt class="py-name">st</tt><tt class="py-op">,</tt><tt class="py-name">tim</tt><tt class="py-op">,</tt><tt class="py-name">upper</tt><tt class="py-op">,</tt><tt class="py-name">st</tt><tt class="py-op">,</tt><tt class="py-name">label</tt><tt class="py-op">=</tt><tt class="py-name">n</tt><tt class="py-op">)</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt>  <tt class="py-line">                <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">fill_between</tt><tt class="py-op">(</tt><tt class="py-name">tim</tt><tt class="py-op">,</tt><tt class="py-name">lower</tt><tt class="py-op">,</tt><tt class="py-name">upper</tt><tt class="py-op">,</tt><tt class="py-name">facecolor</tt><tt class="py-op">=</tt><tt class="py-name">co</tt><tt class="py-op">,</tt><tt class="py-name">alpha</tt><tt class="py-op">=</tt><tt class="py-number">0.12</tt><tt class="py-op">)</tt><tt class="py-comment">#</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt>  <tt class="py-line">            <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt>  <tt class="py-line">                <tt class="py-keyword">pass</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">y</tt><tt class="py-op">:</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt>  <tt class="py-line">            <tt class="py-comment">#print y[n].shape, tim.shape</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt>  <tt class="py-line">            <tt class="py-keyword">try</tt><tt class="py-op">:</tt> <tt class="py-comment">#in the last window we run out of date points</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt>  <tt class="py-line">                <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">plot</tt><tt class="py-op">(</tt><tt class="py-name">tim</tt><tt class="py-op">,</tt><tt class="py-name">y</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-string">'^'</tt><tt class="py-op">,</tt><tt class="py-name">label</tt><tt class="py-op">=</tt><tt class="py-name">n</tt><tt class="py-op">+</tt><tt class="py-string">' obs.'</tt><tt class="py-op">)</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt>  <tt class="py-line">            <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt>  <tt class="py-line">                <tt class="py-keyword">pass</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt>  <tt class="py-line">    <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">savefig</tt><tt class="py-op">(</tt><tt class="py-name">title</tt><tt class="py-op">+</tt><tt class="py-string">'.png'</tt><tt class="py-op">)</tt> </tt>
</div><a name="L69"></a><tt class="py-lineno"> 69</tt>  <tt class="py-line"> </tt>
<a name="pred_new_cases"></a><div id="pred_new_cases-def"><a name="L70"></a><tt class="py-lineno"> 70</tt> <a class="py-toggle" href="#" id="pred_new_cases-toggle" onclick="return toggle('pred_new_cases');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.PlotMeld-module.html#pred_new_cases">pred_new_cases</a><tt class="py-op">(</tt><tt class="py-param">obs</tt><tt class="py-op">,</tt><tt class="py-param">series</tt><tt class="py-op">,</tt><tt class="py-param">weeks</tt><tt class="py-op">,</tt><tt class="py-param">names</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-param">title</tt><tt class="py-op">=</tt><tt class="py-string">'Total new cases per window: predicted vs observed'</tt> <tt class="py-op">,</tt><tt class="py-param">ws</tt><tt class="py-op">=</tt><tt class="py-number">7</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="pred_new_cases-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="pred_new_cases-expanded"><a name="L71"></a><tt class="py-lineno"> 71</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt>  <tt class="py-line"><tt class="py-docstring">    Predicted total new cases in a window vs oserved.</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt>  <tt class="py-line">    <tt class="py-name">fig</tt> <tt class="py-op">=</tt><tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">gcf</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt>  <tt class="py-line">    <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">title</tt><tt class="py-op">(</tt><tt class="py-name">title</tt><tt class="py-op">)</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">names</tt><tt class="py-op">:</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt>  <tt class="py-line">        <tt class="py-name">names</tt> <tt class="py-op">=</tt> <tt class="py-name">series</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt>  <tt class="py-line">    <tt class="py-name">ax</tt> <tt class="py-op">=</tt> <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">gca</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-comment">#fig.add_subplot(111)</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt>  <tt class="py-line">    <tt class="py-name">c</tt> <tt class="py-op">=</tt> <tt class="py-name">cycle</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">'b'</tt><tt class="py-op">,</tt><tt class="py-string">'g'</tt><tt class="py-op">,</tt><tt class="py-string">'r'</tt><tt class="py-op">,</tt><tt class="py-string">'c'</tt><tt class="py-op">,</tt><tt class="py-string">'m'</tt><tt class="py-op">,</tt><tt class="py-string">'y'</tt><tt class="py-op">,</tt><tt class="py-string">'k'</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-string">'time'</tt> <tt class="py-keyword">in</tt> <tt class="py-name">obs</tt><tt class="py-op">:</tt> <tt class="py-comment">#setting the xlabel </tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt>  <tt class="py-line">        <tt class="py-name">x</tt> <tt class="py-op">=</tt> <tt class="py-name">date2num</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">obs</tt><tt class="py-op">[</tt><tt class="py-string">'time'</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">ws</tt><tt class="py-op">*</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">weeks</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt>  <tt class="py-line">        <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">xaxis_date</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt>  <tt class="py-line">    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt>  <tt class="py-line">        <tt class="py-name">x</tt> <tt class="py-op">=</tt> <tt class="py-name">arange</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">weeks</tt><tt class="py-op">)</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt>  <tt class="py-line">    <tt class="py-name">sc</tt><tt class="py-op">=</tt> <tt class="py-number">1</tt> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">series</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt><tt class="py-number">1</tt> <tt class="py-keyword">else</tt> <tt class="py-number">5</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt>  <tt class="py-line">    <tt class="py-name">W</tt> <tt class="py-op">=</tt> <tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-number">0.5</tt><tt class="py-op">*</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-number">1.0</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-number">0.5</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">sc</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">names</tt><tt class="py-op">:</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">obs</tt><tt class="py-op">:</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt>  <tt class="py-line">            <tt class="py-name">co</tt> <tt class="py-op">=</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">next</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt>  <tt class="py-line">            <tt class="py-keyword">print</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">)</tt><tt class="py-op">,</tt>  <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">mean</tt><tt class="py-op">(</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">s</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">s</tt> <tt class="py-keyword">in</tt> <tt class="py-name">series</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt>  <tt class="py-name">type</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">)</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt>  <tt class="py-line">            <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">plot</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">x</tt><tt class="py-op">[</tt><tt class="py-number">7</tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">+</tt><tt class="py-name">x</tt><tt class="py-op">.</tt><tt class="py-name">tolist</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-name">mean</tt><tt class="py-op">(</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">s</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">s</tt> <tt class="py-keyword">in</tt> <tt class="py-name">series</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-string">'%s^'</tt><tt class="py-op">%</tt><tt class="py-name">co</tt><tt class="py-op">,</tt> <tt class="py-name">label</tt><tt class="py-op">=</tt><tt class="py-string">"Mean pred. %s"</tt><tt class="py-op">%</tt><tt class="py-name">n</tt><tt class="py-op">)</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt>  <tt class="py-line">            <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">plot</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-name">nansum</tt><tt class="py-op">(</tt><tt class="py-name">obs</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">ws</tt><tt class="py-op">:</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">ws</tt><tt class="py-op">+</tt><tt class="py-name">ws</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">w</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">weeks</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-string">'%s-o'</tt><tt class="py-op">%</tt><tt class="py-name">co</tt><tt class="py-op">,</tt> <tt class="py-name">label</tt><tt class="py-op">=</tt><tt class="py-string">"obs. Prev"</tt><tt class="py-op">)</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt>  <tt class="py-line">            <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">boxplot</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">nansum</tt><tt class="py-op">(</tt><tt class="py-name">s</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">s</tt> <tt class="py-keyword">in</tt> <tt class="py-name">series</tt><tt class="py-op">]</tt> <tt class="py-op">,</tt><tt class="py-name">positions</tt> <tt class="py-op">=</tt> <tt class="py-name">x</tt><tt class="py-op">,</tt> <tt class="py-name">widths</tt><tt class="py-op">=</tt><tt class="py-name">W</tt><tt class="py-op">,</tt><tt class="py-name">notch</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">vert</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt>  <tt class="py-line">    <tt class="py-comment">#P.xlabel('windows')</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt>  <tt class="py-line">    <tt class="py-comment">#ax.legend(loc=0)</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-string">'time'</tt> <tt class="py-keyword">in</tt> <tt class="py-name">obs</tt><tt class="py-op">:</tt>  </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt>  <tt class="py-line">        <tt class="py-name">fig</tt><tt class="py-op">.</tt><tt class="py-name">autofmt_xdate</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L98"></a><tt class="py-lineno"> 98</tt>  <tt class="py-line"> </tt>
<a name="plot_series2"></a><div id="plot_series2-def"><a name="L99"></a><tt class="py-lineno"> 99</tt> <a class="py-toggle" href="#" id="plot_series2-toggle" onclick="return toggle('plot_series2');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.PlotMeld-module.html#plot_series2">plot_series2</a><tt class="py-op">(</tt><tt class="py-param">tim</tt><tt class="py-op">,</tt><tt class="py-param">obs</tt><tt class="py-op">,</tt><tt class="py-param">series</tt><tt class="py-op">,</tt><tt class="py-param">names</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-param">title</tt><tt class="py-op">=</tt><tt class="py-string">'Simulated vs Observed series'</tt><tt class="py-op">,</tt><tt class="py-param">wl</tt><tt class="py-op">=</tt><tt class="py-number">7</tt><tt class="py-op">,</tt><tt class="py-param">lag</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="plot_series2-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="plot_series2-expanded"><a name="L100"></a><tt class="py-lineno">100</tt>  <tt class="py-line">    <tt class="py-name">ser2</tt><tt class="py-op">=</tt><tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">series</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">:</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt>  <tt class="py-line">        <tt class="py-name">ser2</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">concatenate</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">s</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">s</tt> <tt class="py-keyword">in</tt> <tt class="py-name">series</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt>  <tt class="py-line">    <tt class="py-name">ls</tt> <tt class="py-op">=</tt> <tt class="py-name">ser2</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt>  <tt class="py-line">    <tt class="py-name">tim</tt> <tt class="py-op">=</tt> <tt class="py-name">tim</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-name">ls</tt><tt class="py-op">]</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt>  <tt class="py-line">    <tt class="py-comment">#print type (series)#.I.shape</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt>  <tt class="py-line">    <tt class="py-name">fig</tt> <tt class="py-op">=</tt><tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">gcf</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">names</tt><tt class="py-op">:</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt>  <tt class="py-line">        <tt class="py-name">names</tt> <tt class="py-op">=</tt> <tt class="py-name">series</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt>  <tt class="py-line">    <tt class="py-name">c</tt> <tt class="py-op">=</tt> <tt class="py-name">cycle</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">'b'</tt><tt class="py-op">,</tt><tt class="py-string">'g'</tt><tt class="py-op">,</tt><tt class="py-string">'r'</tt><tt class="py-op">,</tt><tt class="py-string">'c'</tt><tt class="py-op">,</tt><tt class="py-string">'m'</tt><tt class="py-op">,</tt><tt class="py-string">'y'</tt><tt class="py-op">,</tt><tt class="py-string">'k'</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">tim</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">datetime</tt><tt class="py-op">.</tt><tt class="py-name">date</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt>  <tt class="py-line">        <tt class="py-name">lag</tt> <tt class="py-op">=</tt> <tt class="py-name">datetime</tt><tt class="py-op">.</tt><tt class="py-name">timedelta</tt><tt class="py-op">(</tt><tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">lag</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">wl</tt><tt class="py-op">)</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt>  <tt class="py-line">    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt>  <tt class="py-line">        <tt class="py-name">lag</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">lag</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">wl</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">names</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt>  <tt class="py-line">        <tt class="py-name">ax</tt> <tt class="py-op">=</tt> <tt class="py-name">fig</tt><tt class="py-op">.</tt><tt class="py-name">add_subplot</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">names</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">i</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt>  <tt class="py-line">        <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">grid</tt><tt class="py-op">(</tt><tt class="py-name">True</tt><tt class="py-op">)</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">tim</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">datetime</tt><tt class="py-op">.</tt><tt class="py-name">date</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt>  <tt class="py-line">            <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">xaxis_date</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt>  <tt class="py-line">        <tt class="py-name">co</tt> <tt class="py-op">=</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">next</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">obs</tt><tt class="py-op">:</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt>  <tt class="py-line">            <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">plot</tt><tt class="py-op">(</tt><tt class="py-name">tim</tt><tt class="py-op">,</tt><tt class="py-name">obs</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">tim</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-string">'o'</tt><tt class="py-op">,</tt> <tt class="py-name">label</tt><tt class="py-op">=</tt><tt class="py-string">r"$Observed\; %s$"</tt><tt class="py-op">%</tt><tt class="py-name">n</tt><tt class="py-op">)</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt>  <tt class="py-line">        <tt class="py-comment">#pdb.set_trace()</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt>  <tt class="py-line">        <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">plot</tt><tt class="py-op">(</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">tim</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-name">lag</tt><tt class="py-op">,</tt><tt class="py-name">median</tt><tt class="py-op">(</tt><tt class="py-name">ser2</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-string">'k-'</tt><tt class="py-op">,</tt> <tt class="py-name">label</tt><tt class="py-op">=</tt><tt class="py-string">r"$median\; %s$"</tt><tt class="py-op">%</tt><tt class="py-name">n</tt><tt class="py-op">)</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt>  <tt class="py-line">        <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">plot</tt><tt class="py-op">(</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">tim</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-name">lag</tt><tt class="py-op">,</tt><tt class="py-name">mean</tt><tt class="py-op">(</tt><tt class="py-name">ser2</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-string">'k--'</tt><tt class="py-op">,</tt> <tt class="py-name">label</tt><tt class="py-op">=</tt><tt class="py-string">r"$mean\; %s$"</tt><tt class="py-op">%</tt><tt class="py-name">n</tt><tt class="py-op">)</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt>  <tt class="py-line">        <tt class="py-name">lower</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">scoreatpercentile</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">,</tt><tt class="py-number">2.5</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">t</tt> <tt class="py-keyword">in</tt> <tt class="py-name">ser2</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">T</tt><tt class="py-op">]</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt>  <tt class="py-line">        <tt class="py-name">upper</tt> <tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">scoreatpercentile</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">,</tt><tt class="py-number">97.5</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">t</tt> <tt class="py-keyword">in</tt> <tt class="py-name">ser2</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">T</tt><tt class="py-op">]</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">series</tt><tt class="py-op">)</tt><tt class="py-op">&gt;</tt><tt class="py-number">1</tt><tt class="py-op">:</tt> <tt class="py-comment">#in the case of iterative simulations</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt>  <tt class="py-line">            <tt class="py-name">dif</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">upper</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">lower</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt>  <tt class="py-line">            <tt class="py-name">dif</tt>  <tt class="py-op">=</tt> <tt class="py-name">dif</tt><tt class="py-op">/</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">dif</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">10</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt>  <tt class="py-line">            <tt class="py-name">pe</tt><tt class="py-op">,</tt> <tt class="py-name">va</tt> <tt class="py-op">=</tt> <tt id="link-0" class="py-name" targets="Function trunk.BIP.Bayes.PlotMeld.peakdet()=trunk.BIP.Bayes.PlotMeld-module.html#peakdet"><a title="trunk.BIP.Bayes.PlotMeld.peakdet" class="py-name" href="#" onclick="return doclink('link-0', 'peakdet', 'link-0');">peakdet</a></tt><tt class="py-op">(</tt><tt class="py-name">dif</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt>  <tt class="py-line">            <tt class="py-name">xp</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">+</tt> <tt class="py-name">pe</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">tolist</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-op">[</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">lower</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt>  <tt class="py-line">            <tt class="py-name">lower</tt> <tt class="py-op">=</tt> <tt class="py-name">interp</tt><tt class="py-op">(</tt><tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">lower</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">xp</tt><tt class="py-op">,</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">lower</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-name">xp</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-comment"># valley-to-valley interpolated band</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt>  <tt class="py-line">            <tt class="py-name">upper</tt> <tt class="py-op">=</tt> <tt class="py-name">interp</tt><tt class="py-op">(</tt><tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">upper</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">xp</tt><tt class="py-op">,</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">upper</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-name">xp</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-comment">#peak-to-peak interpolated band</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt>  <tt class="py-line">        <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">fill_between</tt><tt class="py-op">(</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">tim</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-name">lag</tt><tt class="py-op">,</tt><tt class="py-name">lower</tt><tt class="py-op">,</tt><tt class="py-name">upper</tt><tt class="py-op">,</tt><tt class="py-name">facecolor</tt><tt class="py-op">=</tt><tt class="py-name">co</tt><tt class="py-op">,</tt><tt class="py-name">alpha</tt><tt class="py-op">=</tt><tt class="py-number">0.2</tt><tt class="py-op">)</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt>  <tt class="py-line">        <tt class="py-comment">#ax.fill_between(array(tim)+lag,lower,upper,facecolor='k',alpha=0.1)</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">i</tt> <tt class="py-op">&lt;</tt> <tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">names</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt><tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">xaxis</tt><tt class="py-op">.</tt><tt class="py-name">set_ticklabels</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt>  <tt class="py-line">        <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">legend</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">i</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt>  <tt class="py-line">            <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">set_title</tt><tt class="py-op">(</tt><tt class="py-name">title</tt><tt class="py-op">)</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt>  <tt class="py-line">    <tt class="py-comment">#ax.xaxis.set_visible(True)</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt>  <tt class="py-line">    <tt class="py-comment">#P.title(title)</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt>  <tt class="py-line">    <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">xlabel</tt><tt class="py-op">(</tt><tt class="py-string">'days'</tt><tt class="py-op">)</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">tim</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">datetime</tt><tt class="py-op">.</tt><tt class="py-name">date</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt>  <tt class="py-line">        <tt class="py-name">fig</tt><tt class="py-op">.</tt><tt class="py-name">autofmt_xdate</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L145"></a><tt class="py-lineno">145</tt>  <tt class="py-line">     </tt>
<a name="L146"></a><tt class="py-lineno">146</tt>  <tt class="py-line"> </tt>
<a name="plot_par_series"></a><div id="plot_par_series-def"><a name="L147"></a><tt class="py-lineno">147</tt> <a class="py-toggle" href="#" id="plot_par_series-toggle" onclick="return toggle('plot_par_series');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.PlotMeld-module.html#plot_par_series">plot_par_series</a><tt class="py-op">(</tt><tt class="py-param">tim</tt><tt class="py-op">,</tt><tt class="py-param">ptlist</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="plot_par_series-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="plot_par_series-expanded"><a name="L148"></a><tt class="py-lineno">148</tt>  <tt class="py-line">    <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">figure</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt>  <tt class="py-line">    <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">title</tt><tt class="py-op">(</tt><tt class="py-string">'Parameters temporal variation'</tt><tt class="py-op">)</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt>  <tt class="py-line">    <tt class="py-name">sq</tt> <tt class="py-op">=</tt> <tt class="py-name">sqrt</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">ptlist</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt>  <tt class="py-line">    <tt id="link-1" class="py-name" targets="Variable trunk.BIP.SDE.example.r=trunk.BIP.SDE.example-module.html#r"><a title="trunk.BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-1', 'r', 'link-1');">r</a></tt><tt class="py-op">=</tt> <tt class="py-name">floor</tt><tt class="py-op">(</tt><tt class="py-name">sq</tt><tt class="py-op">)</tt><tt class="py-op">;</tt><tt class="py-name">c</tt><tt class="py-op">=</tt><tt class="py-name">ceil</tt><tt class="py-op">(</tt><tt class="py-name">sq</tt><tt class="py-op">)</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt><tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">ptlist</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt>  <tt class="py-line">        <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">subplot</tt><tt class="py-op">(</tt><tt id="link-2" class="py-name"><a title="trunk.BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-2', 'r', 'link-1');">r</a></tt><tt class="py-op">,</tt><tt class="py-name">c</tt><tt class="py-op">,</tt><tt class="py-name">i</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt>  <tt class="py-line">        <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">boxplot</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">s</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">s</tt> <tt class="py-keyword">in</tt> <tt class="py-name">ptlist</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">notch</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">positions</tt><tt class="py-op">=</tt><tt class="py-name">tim</tt><tt class="py-op">,</tt><tt class="py-name">vert</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt>  <tt class="py-line">        <tt class="py-comment">#P.errorbar(tim,[median(t[n]) for t in ptlist],yerr=[std(t[n]) for t in ptlist],label=n)</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt>  <tt class="py-line">        <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">ylabel</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">)</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt>  <tt class="py-line">    <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">xlabel</tt><tt class="py-op">(</tt><tt class="py-string">'Windows'</tt><tt class="py-op">)</tt> </tt>
</div><a name="L158"></a><tt class="py-lineno">158</tt>  <tt class="py-line"> </tt>
<a name="plot_par_violin"></a><div id="plot_par_violin-def"><a name="L159"></a><tt class="py-lineno">159</tt> <a class="py-toggle" href="#" id="plot_par_violin-toggle" onclick="return toggle('plot_par_violin');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.PlotMeld-module.html#plot_par_violin">plot_par_violin</a><tt class="py-op">(</tt><tt class="py-param">tim</tt><tt class="py-op">,</tt><tt class="py-param">ptlist</tt><tt class="py-op">,</tt> <tt class="py-param">priors</tt><tt class="py-op">=</tt><tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">,</tt> <tt class="py-param">bp</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="plot_par_violin-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="plot_par_violin-expanded"><a name="L160"></a><tt class="py-lineno">160</tt>  <tt class="py-line">    <tt class="py-name">fig</tt> <tt class="py-op">=</tt> <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">figure</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt>  <tt class="py-line">    <tt class="py-comment">#P.title('Parameters temporal variation')</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt>  <tt class="py-line">    <tt class="py-name">sq</tt> <tt class="py-op">=</tt> <tt class="py-name">sqrt</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">ptlist</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt>  <tt class="py-line">    <tt class="py-name">ad</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> <tt class="py-keyword">if</tt> <tt class="py-name">sq</tt><tt class="py-op">%</tt><tt class="py-number">1</tt> <tt class="py-op">&gt;</tt><tt class="py-number">0.5</tt> <tt class="py-keyword">else</tt> <tt class="py-number">0</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt>  <tt class="py-line">    <tt id="link-3" class="py-name"><a title="trunk.BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-3', 'r', 'link-1');">r</a></tt><tt class="py-op">=</tt> <tt class="py-name">floor</tt><tt class="py-op">(</tt><tt class="py-name">sq</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-name">ad</tt><tt class="py-op">;</tt><tt class="py-name">c</tt><tt class="py-op">=</tt><tt class="py-name">ceil</tt><tt class="py-op">(</tt><tt class="py-name">sq</tt><tt class="py-op">)</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">ptlist</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">3</tt><tt class="py-op">:</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt>  <tt class="py-line">        <tt id="link-4" class="py-name"><a title="trunk.BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-4', 'r', 'link-1');">r</a></tt> <tt class="py-op">=</tt> <tt class="py-number">3</tt><tt class="py-op">;</tt> <tt class="py-name">c</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">priors</tt><tt class="py-op">:</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">tim</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">datetime</tt><tt class="py-op">.</tt><tt class="py-name">date</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt>  <tt class="py-line">            <tt class="py-name">pdate</tt> <tt class="py-op">=</tt> <tt class="py-name">tim</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">datetime</tt><tt class="py-op">.</tt><tt class="py-name">timedelta</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">tim</tt><tt class="py-op">)</tt><tt class="py-op">==</tt><tt class="py-number">1</tt> <tt class="py-keyword">else</tt> <tt class="py-name">tim</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-op">(</tt><tt class="py-name">tim</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">tim</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt>  <tt class="py-line">            <tt class="py-name">tim</tt> <tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-name">pdate</tt><tt class="py-op">]</tt><tt class="py-op">+</tt><tt class="py-name">tim</tt><tt class="py-op">.</tt><tt class="py-name">tolist</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">tim</tt><tt class="py-op">)</tt><tt class="py-op">==</tt><tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt>  <tt class="py-line">                <tt class="py-name">tim</tt>  <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt>  <tt class="py-line">            <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt>  <tt class="py-line">                <tt class="py-name">tim</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">tim</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-op">(</tt><tt class="py-name">tim</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">tim</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">+</tt><tt class="py-name">tim</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt><tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">ptlist</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt>  <tt class="py-line">        <tt class="py-name">ax</tt> <tt class="py-op">=</tt> <tt class="py-name">fig</tt><tt class="py-op">.</tt><tt class="py-name">add_subplot</tt><tt class="py-op">(</tt><tt id="link-5" class="py-name"><a title="trunk.BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-5', 'r', 'link-1');">r</a></tt><tt class="py-op">,</tt><tt class="py-name">c</tt><tt class="py-op">,</tt><tt class="py-name">i</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt>  <tt class="py-line">        <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">grid</tt><tt class="py-op">(</tt><tt class="py-name">True</tt><tt class="py-op">)</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt>  <tt class="py-line">        <tt id="link-6" class="py-name" targets="Function trunk.BIP.Bayes.PlotMeld.violin_plot()=trunk.BIP.Bayes.PlotMeld-module.html#violin_plot"><a title="trunk.BIP.Bayes.PlotMeld.violin_plot" class="py-name" href="#" onclick="return doclink('link-6', 'violin_plot', 'link-6');">violin_plot</a></tt><tt class="py-op">(</tt><tt class="py-name">ax</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-name">priors</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">+</tt><tt class="py-op">[</tt><tt class="py-name">s</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">s</tt> <tt class="py-keyword">in</tt> <tt class="py-name">ptlist</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">tim</tt><tt class="py-op">,</tt><tt class="py-name">bp</tt><tt class="py-op">,</tt> <tt class="py-name">True</tt><tt class="py-op">)</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt>  <tt class="py-line">        <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">ylabel</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">)</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt>  <tt class="py-line">    <tt class="py-comment">#P.xlabel('Windows')</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">tim</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">datetime</tt><tt class="py-op">.</tt><tt class="py-name">date</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt>  <tt class="py-line">        <tt class="py-name">fig</tt><tt class="py-op">.</tt><tt class="py-name">autofmt_xdate</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L184"></a><tt class="py-lineno">184</tt>  <tt class="py-line"> </tt>
<a name="violin_plot"></a><div id="violin_plot-def"><a name="L185"></a><tt class="py-lineno">185</tt> <a class="py-toggle" href="#" id="violin_plot-toggle" onclick="return toggle('violin_plot');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.PlotMeld-module.html#violin_plot">violin_plot</a><tt class="py-op">(</tt><tt class="py-param">ax</tt><tt class="py-op">,</tt><tt class="py-param">data</tt><tt class="py-op">,</tt><tt class="py-param">positions</tt><tt class="py-op">,</tt><tt class="py-param">bp</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">,</tt> <tt class="py-param">prior</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="violin_plot-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="violin_plot-expanded"><a name="L186"></a><tt class="py-lineno">186</tt>  <tt class="py-line">    <tt class="py-docstring">'''</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt>  <tt class="py-line"><tt class="py-docstring">    Create violin plots on an axis</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt>  <tt class="py-line"><tt class="py-docstring">    :Parameters:</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt>  <tt class="py-line"><tt class="py-docstring">        - `ax`: A subplot object</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt>  <tt class="py-line"><tt class="py-docstring">        - `data`: A list of data sets to plot</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt>  <tt class="py-line"><tt class="py-docstring">        - `positions`: x values to position the violins. Can be datetime.date objects.</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt>  <tt class="py-line"><tt class="py-docstring">        - `bp`: Whether to plot the boxplot on top.</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt>  <tt class="py-line"><tt class="py-docstring">        - `prior`: whether the first element of data is a Prior distribution.</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt>  <tt class="py-line"><tt class="py-docstring">    '''</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt>  <tt class="py-line">    <tt class="py-name">sc</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt>  <tt class="py-line">    <tt class="py-name">dist</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">positions</tt><tt class="py-op">)</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">positions</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">datetime</tt><tt class="py-op">.</tt><tt class="py-name">date</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt>  <tt class="py-line">        <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">xaxis_date</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt>  <tt class="py-line">        <tt class="py-name">positions</tt> <tt class="py-op">=</tt> <tt class="py-name">date2num</tt><tt class="py-op">(</tt><tt class="py-name">positions</tt><tt class="py-op">)</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt>  <tt class="py-line">        <tt class="py-name">sc</tt> <tt class="py-op">=</tt> <tt class="py-number">5</tt> <tt class="py-keyword">if</tt> <tt class="py-op">(</tt><tt class="py-name">dist</tt><tt class="py-op">&gt;</tt><tt class="py-number">2</tt> <tt class="py-op">)</tt> <tt class="py-keyword">else</tt> <tt class="py-number">1</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt>  <tt class="py-line">        <tt class="py-comment">#print sc</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt>  <tt class="py-line">    <tt class="py-name">w</tt> <tt class="py-op">=</tt> <tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-number">0.5</tt><tt class="py-op">*</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">dist</tt><tt class="py-op">,</tt><tt class="py-number">1.0</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-number">0.5</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">sc</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt>  <tt class="py-line">    <tt class="py-name">i</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt>  <tt class="py-line">     </tt>
<a name="L206"></a><tt class="py-lineno">206</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">d</tt><tt class="py-op">,</tt><tt class="py-name">p</tt>  <tt class="py-keyword">in</tt> <tt class="py-name">zip</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">positions</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">prior</tt> <tt class="py-keyword">and</tt> <tt class="py-name">i</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt>  <tt class="py-line">            <tt class="py-name">color</tt> <tt class="py-op">=</tt> <tt class="py-string">'g'</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt>  <tt class="py-line">            <tt class="py-name">color</tt> <tt class="py-op">=</tt> <tt class="py-string">'y'</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt>  <tt class="py-line">        <tt class="py-name">k</tt> <tt class="py-op">=</tt> <tt class="py-name">gaussian_kde</tt><tt class="py-op">(</tt><tt class="py-name">d</tt><tt class="py-op">)</tt> <tt class="py-comment">#calculates the kernel density</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt>  <tt class="py-line">        <tt class="py-name">m</tt> <tt class="py-op">=</tt> <tt class="py-name">k</tt><tt class="py-op">.</tt><tt class="py-name">dataset</tt><tt class="py-op">.</tt><tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-comment">#lower bound of violin</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt>  <tt class="py-line">        <tt id="link-7" class="py-name" targets="Variable trunk.BIP.SDE.example.M=trunk.BIP.SDE.example-module.html#M"><a title="trunk.BIP.SDE.example.M" class="py-name" href="#" onclick="return doclink('link-7', 'M', 'link-7');">M</a></tt> <tt class="py-op">=</tt> <tt class="py-name">k</tt><tt class="py-op">.</tt><tt class="py-name">dataset</tt><tt class="py-op">.</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-comment">#upper bound of violin</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt>  <tt class="py-line">        <tt class="py-name">x</tt> <tt class="py-op">=</tt> <tt class="py-name">arange</tt><tt class="py-op">(</tt><tt class="py-name">m</tt><tt class="py-op">,</tt><tt id="link-8" class="py-name"><a title="trunk.BIP.SDE.example.M" class="py-name" href="#" onclick="return doclink('link-8', 'M', 'link-7');">M</a></tt><tt class="py-op">,</tt><tt class="py-op">(</tt><tt id="link-9" class="py-name"><a title="trunk.BIP.SDE.example.M" class="py-name" href="#" onclick="return doclink('link-9', 'M', 'link-7');">M</a></tt><tt class="py-op">-</tt><tt class="py-name">m</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-number">100.</tt><tt class="py-op">)</tt> <tt class="py-comment"># support for violin</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt>  <tt class="py-line">        <tt class="py-name">v</tt> <tt class="py-op">=</tt> <tt class="py-name">k</tt><tt class="py-op">.</tt><tt class="py-name">evaluate</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">)</tt> <tt class="py-comment">#violin profile (density curve)</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt>  <tt class="py-line">        <tt class="py-name">v</tt> <tt class="py-op">=</tt> <tt class="py-name">v</tt><tt class="py-op">/</tt><tt class="py-name">v</tt><tt class="py-op">.</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">w</tt> <tt class="py-comment">#scaling the violin to the available space</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt>  <tt class="py-line">        <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">fill_betweenx</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">p</tt><tt class="py-op">,</tt><tt class="py-name">v</tt><tt class="py-op">+</tt><tt class="py-name">p</tt><tt class="py-op">,</tt><tt class="py-name">facecolor</tt><tt class="py-op">=</tt><tt class="py-name">color</tt><tt class="py-op">,</tt><tt class="py-name">alpha</tt><tt class="py-op">=</tt><tt class="py-number">0.3</tt><tt class="py-op">)</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt>  <tt class="py-line">        <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">fill_betweenx</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">p</tt><tt class="py-op">,</tt><tt class="py-op">-</tt><tt class="py-name">v</tt><tt class="py-op">+</tt><tt class="py-name">p</tt><tt class="py-op">,</tt><tt class="py-name">facecolor</tt><tt class="py-op">=</tt><tt class="py-name">color</tt><tt class="py-op">,</tt><tt class="py-name">alpha</tt><tt class="py-op">=</tt><tt class="py-number">0.3</tt><tt class="py-op">)</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt>  <tt class="py-line">        <tt class="py-name">i</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">bp</tt><tt class="py-op">:</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt>  <tt class="py-line">        <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">boxplot</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt><tt class="py-name">notch</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">positions</tt><tt class="py-op">=</tt><tt class="py-name">positions</tt><tt class="py-op">,</tt><tt class="py-name">widths</tt><tt class="py-op">=</tt><tt class="py-name">w</tt><tt class="py-op">,</tt> <tt class="py-name">vert</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
</div><a name="L222"></a><tt class="py-lineno">222</tt>  <tt class="py-line"> </tt>
<a name="peakdet"></a><div id="peakdet-def"><a name="L223"></a><tt class="py-lineno">223</tt> <a class="py-toggle" href="#" id="peakdet-toggle" onclick="return toggle('peakdet');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.PlotMeld-module.html#peakdet">peakdet</a><tt class="py-op">(</tt><tt class="py-param">v</tt><tt class="py-op">,</tt> <tt class="py-param">delta</tt><tt class="py-op">,</tt> <tt class="py-param">x</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="peakdet-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="peakdet-expanded"><a name="L224"></a><tt class="py-lineno">224</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt>  <tt class="py-line"><tt class="py-docstring">    Converted from MATLAB script at http://billauer.co.il/peakdet.html</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt>  <tt class="py-line"><tt class="py-docstring">    Currently returns two lists of tuples, but maybe arrays would be better</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt>  <tt class="py-line"><tt class="py-docstring">    function [maxtab, mintab]=peakdet(v, delta, x)</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt>  <tt class="py-line"><tt class="py-docstring">    %PEAKDET Detect peaks in a vector</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt>  <tt class="py-line"><tt class="py-docstring">    % [MAXTAB, MINTAB] = PEAKDET(V, DELTA) finds the local</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt>  <tt class="py-line"><tt class="py-docstring">    % maxima and minima ("peaks") in the vector V.</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt>  <tt class="py-line"><tt class="py-docstring">    % MAXTAB and MINTAB consists of two columns. Column 1</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt>  <tt class="py-line"><tt class="py-docstring">    % contains indices in V, and column 2 the found values.</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt>  <tt class="py-line"><tt class="py-docstring">    %</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt>  <tt class="py-line"><tt class="py-docstring">    % With [MAXTAB, MINTAB] = PEAKDET(V, DELTA, X) the indices</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt>  <tt class="py-line"><tt class="py-docstring">    % in MAXTAB and MINTAB are replaced with the corresponding</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt>  <tt class="py-line"><tt class="py-docstring">    % X-values.</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt>  <tt class="py-line"><tt class="py-docstring">    %</tt> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt>  <tt class="py-line"><tt class="py-docstring">    % A point is considered a maximum peak if it has the maximal</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt>  <tt class="py-line"><tt class="py-docstring">    % value, and was preceded (to the left) by a value lower by</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt>  <tt class="py-line"><tt class="py-docstring">    % DELTA.</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt>  <tt class="py-line"><tt class="py-docstring">    % Eli Billauer, 3.4.05 (Explicitly not copyrighted).</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt>  <tt class="py-line"><tt class="py-docstring">    % This function is released to the public domain; Any use is allowed.</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt>  <tt class="py-line">    <tt class="py-name">maxtab</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt>  <tt class="py-line">    <tt class="py-name">mintab</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt>  <tt class="py-line">        </tt>
<a name="L247"></a><tt class="py-lineno">247</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">x</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt>  <tt class="py-line">        <tt class="py-name">x</tt> <tt class="py-op">=</tt> <tt class="py-name">arange</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">v</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt>  <tt class="py-line">     </tt>
<a name="L250"></a><tt class="py-lineno">250</tt>  <tt class="py-line">    <tt class="py-name">v</tt> <tt class="py-op">=</tt> <tt class="py-name">asarray</tt><tt class="py-op">(</tt><tt class="py-name">v</tt><tt class="py-op">)</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt>  <tt class="py-line">     </tt>
<a name="L252"></a><tt class="py-lineno">252</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">v</tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt>  <tt class="py-line">        <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">exit</tt><tt class="py-op">(</tt><tt class="py-string">'Input vectors v and x must have same length'</tt><tt class="py-op">)</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt>  <tt class="py-line">     </tt>
<a name="L255"></a><tt class="py-lineno">255</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">isscalar</tt><tt class="py-op">(</tt><tt class="py-name">delta</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt>  <tt class="py-line">        <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">exit</tt><tt class="py-op">(</tt><tt class="py-string">'Input argument delta must be a scalar'</tt><tt class="py-op">)</tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt>  <tt class="py-line">     </tt>
<a name="L258"></a><tt class="py-lineno">258</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">delta</tt> <tt class="py-op">&lt;=</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt>  <tt class="py-line">        <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">exit</tt><tt class="py-op">(</tt><tt class="py-string">'Input argument delta must be positive'</tt><tt class="py-op">)</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt>  <tt class="py-line">     </tt>
<a name="L261"></a><tt class="py-lineno">261</tt>  <tt class="py-line">    <tt class="py-name">mn</tt><tt class="py-op">,</tt> <tt class="py-name">mx</tt> <tt class="py-op">=</tt> <tt class="py-name">Inf</tt><tt class="py-op">,</tt> <tt class="py-op">-</tt><tt class="py-name">Inf</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt>  <tt class="py-line">    <tt class="py-name">mnpos</tt><tt class="py-op">,</tt> <tt class="py-name">mxpos</tt> <tt class="py-op">=</tt> <tt class="py-name">NaN</tt><tt class="py-op">,</tt> <tt class="py-name">NaN</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt>  <tt class="py-line">     </tt>
<a name="L264"></a><tt class="py-lineno">264</tt>  <tt class="py-line">    <tt class="py-name">lookformax</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt>  <tt class="py-line">     </tt>
<a name="L266"></a><tt class="py-lineno">266</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">arange</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">v</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt>  <tt class="py-line">        <tt class="py-name">this</tt> <tt class="py-op">=</tt> <tt class="py-name">v</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">this</tt> <tt class="py-op">&gt;</tt> <tt class="py-name">mx</tt><tt class="py-op">:</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt>  <tt class="py-line">            <tt class="py-name">mx</tt> <tt class="py-op">=</tt> <tt class="py-name">this</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt>  <tt class="py-line">            <tt class="py-name">mxpos</tt> <tt class="py-op">=</tt> <tt class="py-name">x</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">this</tt> <tt class="py-op">&lt;</tt> <tt class="py-name">mn</tt><tt class="py-op">:</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt>  <tt class="py-line">            <tt class="py-name">mn</tt> <tt class="py-op">=</tt> <tt class="py-name">this</tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt>  <tt class="py-line">            <tt class="py-name">mnpos</tt> <tt class="py-op">=</tt> <tt class="py-name">x</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt>  <tt class="py-line">         </tt>
<a name="L275"></a><tt class="py-lineno">275</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">lookformax</tt><tt class="py-op">:</tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">this</tt> <tt class="py-op">&lt;</tt> <tt class="py-name">mx</tt><tt class="py-op">-</tt><tt class="py-name">delta</tt><tt class="py-op">:</tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt>  <tt class="py-line">                <tt class="py-name">maxtab</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">mxpos</tt><tt class="py-op">,</tt> <tt class="py-name">mx</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt>  <tt class="py-line">                <tt class="py-name">mn</tt> <tt class="py-op">=</tt> <tt class="py-name">this</tt> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt>  <tt class="py-line">                <tt class="py-name">mnpos</tt> <tt class="py-op">=</tt> <tt class="py-name">x</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt>  <tt class="py-line">                <tt class="py-name">lookformax</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">this</tt> <tt class="py-op">&gt;</tt> <tt class="py-name">mn</tt><tt class="py-op">+</tt><tt class="py-name">delta</tt><tt class="py-op">:</tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt>  <tt class="py-line">                <tt class="py-name">mintab</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">mnpos</tt><tt class="py-op">,</tt> <tt class="py-name">mn</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt>  <tt class="py-line">                <tt class="py-name">mx</tt> <tt class="py-op">=</tt> <tt class="py-name">this</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt>  <tt class="py-line">                <tt class="py-name">mxpos</tt> <tt class="py-op">=</tt> <tt class="py-name">x</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt>  <tt class="py-line">                <tt class="py-name">lookformax</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt>  <tt class="py-line">  </tt>
<a name="L288"></a><tt class="py-lineno">288</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">maxtab</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">mintab</tt><tt class="py-op">)</tt> </tt>
</div><a name="L289"></a><tt class="py-lineno">289</tt>  <tt class="py-line"> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt>  <tt class="py-line"><tt class="py-keyword">if</tt> <tt class="py-name">__name__</tt> <tt class="py-op">==</tt> <tt class="py-string">"__main__"</tt><tt class="py-op">:</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt>  <tt class="py-line">    <tt class="py-keyword">print</tt> <tt class="py-string">"Hello World"</tt><tt class="py-op">;</tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt>  <tt class="py-line"> </tt><script type="text/javascript">
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